[BioC] zlibbioc on Window -- was: Help installing 'rhdf5' in an "offline" environment

Bernd Fischer bernd.fischer at embl.de
Wed Jul 30 20:52:55 CEST 2014


Dear Ole!

Did you try to install the Windows binary package?
zlibbioc_1.10.0.zip (32- & 64-bit)

Bernd
On 30.07.2014, at 14:05, Wolfgang Huber <whuber at embl.de> wrote:

> Ole
> 
> sounds like a challenging environment.
> Did you check the vignette of the zlibbioc package (available from http://www.bioconductor.org/packages/release/bioc/html/zlibbioc.html ) - perhaps you need to go into the configure file zlibbioc/src/zlib-1.2.5/configure and adapt.
> And/or, run the configure manually and see where it fails (it looks like the output you posted is truncated / missing important information).
> 
> Wolfgang
> 
> 
> 
> 
> 
> 
> 
> Il giorno Jul 30, 2014, alle ore 6:01 EDT, Ole Rogeberg <ole.rogeberg at gmail.com> ha scritto:
> 
>> I would like to install rhdf5 in a secured, Windows-based server
>> environment that (for security reasons) cannot access outside servers or
>> websites. As the environment is "offline" in this sense, I cannot use the
>> recommended procedure involving biocLite.R and the bioconductor repository
>> directly for installing the rhdf5 package.
>> 
>> I can upload specific files to the offline environment, but not install
>> software directly myself (lack write-access to the relevant folders on the
>> server where software is located). However, the system administrator has
>> placed a mirror of CRAN in the "offline" environment, and installing new
>> CRAN packages in R is unproblematic.
>> 
>> For rhdf5 I have tried:
>> 
>> 1. Install rhdf5 directly: Uploading the rhdf5_2.8.0.tar.gz file and
>> installing it from the package manager in RStudio. This gives the message
>> that "ERROR: dependency 'zlibbioc' is not available for package 'rhdf5'"
>> 
>> 2. Installing required packages that rhdf5 relies on: Uploading and
>> installing zlibbioc in the same manner. This gives me a warning that "This
>> package has a configure script. It probably needs manual configuration" -
>> followed by a compilation error (see full R-message here
>> <http://screencast.com/t/2bTXvwuZ>).
>> 
>> I am unable to figure out what the "status 127" error message refers to, or
>> if this is even a sensible way to proceed.
>> 
>> Has anyone got a simple solution that I can implement or (if needed) a more
>> technical solution I can forward to my system administrator?
>> 
>> Sincerely,
>> 
>> Ole Rogeberg
>> 
>> 	[[alternative HTML version deleted]]
>> 
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